Articles
Complete genome sequence of shamrock chlorotic ringspot virus, a novel Potyvirus infecting ornamental Oxalis triangularis in the United States and the Netherlands
Article number
1392_6
Pages
45 – 52
Language
English
Abstract
Ornamental Oxalis, commonly known as the Shamrock plant, is grown as a potted plant in the United States and The Netherlands, especially for marketing in the spring around St.
Patricks Day in the US. A Potyvirus causing chlorotic ringspot in ornamental Oxalis regnellii was first described in Washington (WA) in 1981. Plants showing similar symptoms and Potyvirus particles were reported in New York (NY, 2009) and Florida (FL, 2012). The name shamrock chlorotic ringspot virus (SCRV) was coined. Potyvirus-like filamentous virus particles were observed in leaf samples showing similar symptoms from Oxalis triangularis (syn. of Oxalis regnellii) plants from Wisconsin (WI, 2012-2013). A total RNA extract from partially purified virion preparations from symptomatic tissue was used as the template for a random PCR to produce a cDNA library.
The near complete nucleotide sequence of SCRV-WI was obtained from multiple overlapping cDNA clones, coupled with 5 and 3 RACE cloning, and determined to be 10,120 nucleotides.
Several oxalis plants in the in vivo collection at the Plant Protection Organization of the Netherlands (NPPO-NL) exhibiting similar symptoms tested positive in 2010 for Potyvirus using generic potyviral primers.
In 2021, RNAseq analysis of a cDNA library sequenced on the NovaSeq 6000 platform revealed the presence of a 10,136 nt genome sequence, which showed 98.5% identity with the SCMV-WI isolate.
The SCRV-WI and SCRV-NPPO-NL isolates each contain one large open reading frame (ORF) encoding a polyprotein of 3,276 amino acids (aa) and the small P3N-PIPO fusion protein (70 aa) following a translational frameshift.
SCRV shared the highest sequence identities with members of the genus Potyvirus, with less than 53 and 47% identities for the genome and polyprotein, respectively.
Based on the predicted polyprotein cleavage sites, the number and size of the predicted processed mature peptides, and phylogenetic relatedness to members of the family Potyviridae, SCRV appears to be a new species in the genus Potyvirus. We propose the species name Potyvirus oxalis for this new member of the Potyviridae.
Patricks Day in the US. A Potyvirus causing chlorotic ringspot in ornamental Oxalis regnellii was first described in Washington (WA) in 1981. Plants showing similar symptoms and Potyvirus particles were reported in New York (NY, 2009) and Florida (FL, 2012). The name shamrock chlorotic ringspot virus (SCRV) was coined. Potyvirus-like filamentous virus particles were observed in leaf samples showing similar symptoms from Oxalis triangularis (syn. of Oxalis regnellii) plants from Wisconsin (WI, 2012-2013). A total RNA extract from partially purified virion preparations from symptomatic tissue was used as the template for a random PCR to produce a cDNA library.
The near complete nucleotide sequence of SCRV-WI was obtained from multiple overlapping cDNA clones, coupled with 5 and 3 RACE cloning, and determined to be 10,120 nucleotides.
Several oxalis plants in the in vivo collection at the Plant Protection Organization of the Netherlands (NPPO-NL) exhibiting similar symptoms tested positive in 2010 for Potyvirus using generic potyviral primers.
In 2021, RNAseq analysis of a cDNA library sequenced on the NovaSeq 6000 platform revealed the presence of a 10,136 nt genome sequence, which showed 98.5% identity with the SCMV-WI isolate.
The SCRV-WI and SCRV-NPPO-NL isolates each contain one large open reading frame (ORF) encoding a polyprotein of 3,276 amino acids (aa) and the small P3N-PIPO fusion protein (70 aa) following a translational frameshift.
SCRV shared the highest sequence identities with members of the genus Potyvirus, with less than 53 and 47% identities for the genome and polyprotein, respectively.
Based on the predicted polyprotein cleavage sites, the number and size of the predicted processed mature peptides, and phylogenetic relatedness to members of the family Potyviridae, SCRV appears to be a new species in the genus Potyvirus. We propose the species name Potyvirus oxalis for this new member of the Potyviridae.
Authors
R. Jordan, M.A. Guaragna, B. Lockhart, C. Oplaat, M. Botermans, P. de Koning, E. Meekes, D. Mollov
Keywords
false shamrock, high-throughput sequencing, Potyvirus, Potyviridae
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